[clangd] Add a flag for spelled references in the Index

This patch allows the index does to provide a way to distinguish
implicit references (e.g. coming from macro expansions) from the spelled
ones. The corresponding flag was added to RefKind and symbols that are
referenced without spelling their name explicitly are now marked
implicit. This allows fixing incorrect behavior when renaming a symbol
that was referenced in macro expansions would try to rename macro
invocations.

Differential Revision: D72746

Reviewed by: hokein